An Algorithm for RNA Pseudoknots
M. Pillsbury, J. A. Taylor, H. Orland, A. Zee
Abstract
We further develop the large N formalism presented by some of us in earlier works in order to recursively calculate the partition function of a singly pseudoknotted RNA. We demonstrate that this calculation takes time proportional to the sixth power of the length of the RNA. The algorithm itself is presented in a self-contained form for the convenience of readers interested in implementing it.
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